There are a way to align phage reads in to bacterial genomes?

Question

[schlogl]

Hi guys. Can I use bwa, star or any alignment prog to try to align some phage reads/dna against bacterial genomes? I though It could be interesting way to search for foreign dna in bacteria. What your thoughts about it? Or it is more easy to use any tool out there? Thanks. Paulo

PS- I ask because I use some chr dna from an Actinobacter in Blast searches against the virus database and I found a lot of phages sequences with high similarity to this bacterial genome.

Answer 1

[GenoMax]

Can I use bwa, star or any alignment prog to try to align some phage reads/dna against bacterial genomes?

Aligners are data agnostic so they can use data from any source. Any aligner would work for this purpose as long as you are comfortable with command line. bwa or bbmap from BBMap suite would be fine to use.

I found a lot of phages sequences with high similarity to this bacterial genome.

Bacteriophages infect bacteria and can integrate into bacterial genomes. It is not surprising to find sequences with similarity to them in bacterial genomes. Phages are responsible for horizontal gene transfer and are drivers of evolution. e.g. https://pmc.ncbi.nlm.nih.gov/articles/PMC515249

[schlogl]

Thanks GenoMax